#pragma once

#include <ScoringScheme.h>
#include <ScoringS2S.h>
#include <SubMatrix.h>
#include <SequenceData.h>
#include <NWAlign.h>
#include <Align.h>
#include <AGPFunction.h>
#include "UpgmaCluster.h"

using namespace Biopool;

class MultiScoringScheme : public ScoringScheme
{
public:
	MultiScoringScheme(SubMatrix *, AlignmentData *, Structure *, vector< vector<Biopool::Align*> >, UpgmaCluster* , vector<string> );
	~MultiScoringScheme();

	vector< vector<Biopool::Align*> > alignments;
	vector<string> sequences;
	UpgmaCluster* uc;

	virtual double scoring(int, int);
	virtual ScoringScheme* newCopy();
};

